This is a known issue that will likely never be officially fixed. It appears to have been a result of the manufacturers making a hardware change without rewriting the emulators to compensate. The Neo Geo scaling issue is the most serious result, though the GBA emu was also affected in a different manner. The Neo Geo scaling problem still exists on the A330, which is what makes me believe it will never be officially fixed -- they could/should have fixed it with the A330 but didn't.
If you install Dingux, you can use the FBA emulator to play Neo Geo games without any scaling issues at all.